evenness: Taxonomic/phylogenetic/functional evenness of species or...

In BAT: Biodiversity Assessment Tools

Taxonomic/phylogenetic/functional evenness of species or individuals.

Description

Regularity of abundances and distances (if PD/FD) between species in a community.

Usage

evenness(
  comm,
  tree,
  distance,
  method = "expected",
  func = "camargo",
  abund = TRUE
)

Arguments

comm	A sites x species matrix, with either abundance or incidence data. If missing, the evenness using the full tree or distance matrix is calculated.
tree	A phylo or hclust object (used only for PD or FD) or alternatively a species x traits matrix or data.frame to build a functional tree.
distance	A dist or matrix object representing the phylogenetic or functional distance between species. If both tree and distance are missing, taxonomic evenness is calculated.
method	Calculate evenness using "expected" values (default) or values based on "contribution" of species to the tree.
func	Calculate evenness using "Camargo" (default) or "Bulla" index.
abund	A boolean (T/F) indicating whether evenness should be calculated using abundance data.

Details

Evenness is calculated based on the index of Camargo (1993) or Bulla (1994) using the values of both species abundances and edge lengths in the tree (if PD/FD).

If no tree or distance is provided the result is the original index.

If any site has < 2 species its value will be NA.

Value

A vector of values per site (or a single value if no comm is given).

References

Bulla, L. (1994) An index of evenness and its associated diversity measure. Oikos, 70: 167-171.

Camargo, J.A. (1993) Must dominance increase with the number of subordinate species in competitive interactions? Journal of Theoretical Biology, 161: 537-542.

Examples

comm <- matrix(c(1,2,0,0,0,1,1,0,0,0,0,2,2,0,0,1,1,1,1,100), nrow = 4, byrow = TRUE)
distance <- dist(c(1:5), method = "euclidean")
tree <- hclust(distance, method = "average")
evenness(comm)
evenness(tree = tree, func = "bulla")
evenness(comm, tree)
evenness(comm, tree, method = "contribution")
evenness(comm, tree, abund = FALSE)

BAT documentation built on May 29, 2024, 7:35 a.m.